I'm not entirely sure what skeleton you're using, but there are two things to keep in mind from my findings:
You do not need all the vertex groups to be included anymore. Try deleting some and see if that helps.
If you're using a dev kit from a third-party (i.e. Slink) they may do something funny to the skeleton since they're assuming you have the Avastar plugin. I have tried using their templates directly and come across the same problem you describe.
I would suggest swapping the skeleton you currently have for the one provided by Machanimamatrix (http://blog.machinimatrix.org/fitted_mesh_survival_kit/). Currently I'm still working on finding a "vanilla" Bento skeleton similar to the one I linked above. I have discovered something on the same site (http://blog.machinimatrix.org/avatar-workbench/) but I have not gotten a chance to verify it.
Hopefully this helps. Please post any findings, as I'm sure others have similar questions.
EDIT:
I downloaded the Bento Female listed under "Bento Meshes (Without any warranty)" and replaced the armature from that file with the one in my existing WIP-rigged model. It seems to go in without trouble. I see the "Skin weights" checkbox enabled for me when I upload, as well. See if using that model/armature works for you. You may need to re-parent the model and/or add in the new bone groups.